We presented talks at the Facilitating Anatomy Ontology Interoperability workshop. Jim’s talk was on representing taxa as individuals in OWL, an alternative to the common representation of taxa as classes, which facilitates annotation of phenotypic data involving polymorphism and evolutionary reversals.  I presented a lightning talk on the anatomy ontology synchronization requirements for linking evolutionary and model organism phenotypes.  Other presentations from the workshop are available here. We also presented a poster describing the reasoning used in the Phenoscape Knowledgebase.

The main conference included interesting talks on a broad range of topics including the application of ontologies to proteins, diseases, biological mechanisms, and electronic health records. Presentations can be downloaded here.

The second day focused on applications to biological data and web services.  A discussion on “taxonomic intelligence” was particularly illuminating.  It provided an example of how different communities can share a set of identifiers for species, for example, yet provide their own set of statements about the taxonomy relating those species.  Each community can draw conclusions relevant to its preferred taxonomy using data associated with the same species.

The afternoon focused on the SSWAP project, led by Damian Gessler.  SSWAP is a protocol which uses OWL documents to describe the inputs and outputs relevant to a web service.  Interestingly, users of these web services would submit their input in the very same OWL model used for service descriptions.

In Phenoscape, we are using OBO ontologies rather than RDF and OWL and storing our ontological annotations in OBD, a datastore tailored for OBO technologies which provides its own very effective reasoner.  However, this workshop provided a great opportunity to stay up to date with semantic web standards and explore how to make our data compatible with and part of the global semantic web.  In addition, St. John’s College was a great meeting location – it is a small college with a wonderful natural landscape in the hills outside of Santa Fe.

While the rest of Phenoscape was at the ASIH meeting, involved with the ontology workshop and the release of the database and website, I was across the country, representing Phenoscape at the International Conference on Biomedical Ontologies (ICBO) in Buffalo, NY.  ICBO covered 2-3/4 days (July 24-26) of presentations with two evening poster sessions. There were also software demos during the lunch breaks, and two panel discussions.

Although many of the sessions were devoted to ontologies of disease and clinical practice, there were a number of talks of interest to Phenoscapers. Among these were several alignment talks, including one from the BGEE group on Homolonto and Chris Mungall’s on GO cross products and Uberon.  There were also sessions on annotation and natural language processing (NLP), including Mike Bada’s talk on developing a corpus for testing NLP based annotation. There were also two talks specifically about ontologies and physiology, one by John Gennari focused on integrating existing anatomy ontologies (e.g., FMA) with physiological simulations, though he specifically ducked ontological modeling of physiology as process.  The other was an ‘old school AI’ simulation of a patient, that includes models of physiology, cognition, and NLP.

There was also some promising activity on behavior ontologies, including a poster by Tim Beck, a postdoc from the UK on a mammalian behavior ontology and a “behavior lunch” on the second day, with Tim, Judy Blake, David Shotton (ABO collaborator from Oxford), Mary Shimoyama (RGD), and several others.  There is a European plan to develop a new OWL-based general behavior ontology, and Chris Mungall has recently established an OBO-behavior list.

There was also a lot of discussion generated by the proposed ontology of homology relations, although the consensus from the numerous people I discussed it with was that it needed more work.

Other interesting ontologies included an ontology of Evolutionary processes presented in a poster by Adam Goldstein (Iona University).  He’s since been in contact with Hilmar, and I believe with representatives of CDAO and Dryad.  Phenoscape was also represented by a poster.

There were two panels, one focussing on Ontology and Publishing.  Although the lineup, which included a representative from Elsevier (Jabe Wilson) and Alan Ruttenberg from Science Commons, suggested a discussion on open publishing, the Elsevier representation was quite restrained, and it was Larry Hunter who made the strongest argument that publishers currently provide little value to academics.  David Shotton discussed his semantic annotation of a randomly selected paper on a tropical disease, and there seemed to be consensus that semantic markup ought to be either the author’s or the publisher’s responsibility, rather than the current post-publication markup by project curators.

The second panel was on the future (and past) of ontologies and knowledge representation.  I think the two memorable claims from this discussion were the call to expand the A-box (since the T-box is really less than most people think) and Barry Smith’s claim that in 25 years consulting ontologists will be as common in biology and medical departments as statisticians are today.

The text from all the presentations and posters will be made available at Nature Proceedings.  There was also an ICBO group on FriendFeed with other attendee’s tweets from the conference and preceeding tutorial sessions.  Finally, I will be posting a more detailed report on my personal blog.

Ontologies, controlled vocabularies with well-defined relations among terms, are a key tool in scientific data integration. By using ontologies, scientists from different disciplines can know when they are referring to the same entity by different names, and new discoveries are enabled by computer software being able to reason across disciplines and over large datasets. Already widely used in genomics, ontologies are of growing importance in systematics, ecology, behavior, genetics, morphology and physiology. This workshop aims to explore the utility of ontologies for ichthyology and herpetology, using the Teleost Anatomy Ontology and the Amphibian Anatomy Ontology as case studies of community resources that are being actively developed and used by members of ASIH. Participants will present examples of how these ontologies are being used to provide new ways of exploring data within morphological and phenotypic databases. Talks in the morning will be followed in the afternoon with ontology development workshops and hands-on demonstrations of Phenoscape and AmphibAnat tools.

DATE & TIME: Saturday, July 25, 2009

PLACE: Hilton Portland & Executive Tower

SPEAKERS:

• Hilmar Lapp, National Evolutionary Synthesis Center: A gentle introduction to ontologies for biology
• Monte Westerfield, Director, Zebrafish Information Network and Institute of Neuroscience, Eugene, OR: Linking animal models and human diseases
• Paula Mabee, University of South Dakota: Phenoscape: Using ontologies to link comparative morphology to genes
• Greg Riccardi, Florida State University: Why ontologies are important for understanding morphological images
• Peter Vize, University of Calgary: The Xenopus ontology and database
• Anne Maglia, Missouri University of Science and Technology: Development of an anatomical ontology for amphibians
• Marc Robinson-Rechavi, Universite de Lausanne, France: Integrating ontology and homology for the study of gene expression evolution

The workshop is jointly sponsored by the Phenoscape and AmphibAnat projects (Oganizers: Paula Mabee, Anne Maglia, Professor, Todd Vision and Monte Westerfield).

Phenoscape report from the DECAP meeting (Feb. 27-March 1, 2009)
(Paula Mabee, Wasila Dahdul, Jim Balhoff, Peter Midford)

Phenoscape met in association with the Deep Fin Research Coordination Network, Euteleost Tree of Life (EToL), Cypriniform Tree of Life (CToL), and All Catfish Species Inventory (ACSI), i.e. “DECAP”, in Kansas City February 27-March 1 to discuss “Updates, Resources, and Plans for the Phylogeny of Fishes”. The DeepFin network’s aim is to “build an open and diverse organization, to foster productive collaborations, to develop cyberinfrastructure, and to promote education on fish biodiversity and evolution”, and Phenoscape’s focus on providing an informatics connection among morphological and genetic data types is consistent with this mission.
Phenoscape organized a workshop a day before DECAP to use the gathering of ichthyologists to provide expert input to the Teleost Anatomy Ontology (TAO), to introduce them to the system, and to get feedback on the developing web interface. In attendance were Phenoscapers (Paula Mabee, Phenoscape PI; Wasila Dahdul, Anatomy ontology curator; Jim Balhoff, software and web-interface development; Peter Midford, Taxonomy ontology, liason with Catalog of Fishes), ichthyologists (Gloria Arratia, Terry Grande, Eric Hilton, John Lundberg, Rick Mayden, Mark Sabaj, Ed Wiley) and two graduate students (Jeff Engeman and Sarah Rages).
After introductions, Wasila gave participants a refresher/introduction to the Teleost Anatomy Ontology (TAO). She focused on the form of genus-differentia definitions that are required for ontology terms in preparation for our ontology development session. We sent spreadsheets of terms and other ontology data from two skeletal areas, the gill arches and the lateral line system, to focus on refining term definitions and relationships. These terms are required for curation of systematic characters, and some had been requested by individual curators via the term tracker over the past few months. Jackie Webb provided significant input to the lateral line system terms, and we thank her for this. Our goal was to obtain expert community review of these, focusing on consistency across terms and form and generality of definition.
We broke out into two groups (gill arches, lateral line system), and terms were evaluated one at a time. Additional synonyms and relationships were suggested by the group, definitions were refined and comments added. Some of the terms and definitions that were inherited from the zebrafish anatomical ontology (the TAO was cloned from the Zebrafish Anatomy Ontology in September 2007) required more general definitions. For example the definition for “hyomandibula” read “The hyomandibula is the large, dorsal-most member of the hyoid arch. It begins ossifying in the dorsal edge of the hyosymplectic cartilage near the hyomandibular foramen (4.6 mm NL). Ossification spreads through the cartilage, and sheets of membrane bone form off the cartilage model anteriorly and posteriorly (6.6 mm). In the adult, the hyomandibula has cartilage-capped anterior and posterior articulating heads that meet the sphenotic-prootic fossa and the pterotic fossa, respectively, in synovial joints. A posterior knob of bone develops, also capped in cartilage, and it forms a synovial joint with the opercle.” We recognized that the developmental information was not appropriate for the TAO because it applies to only zebrafish and internally suggested a new definition: “Endochondral bone that is bilaterally paired and articulates with the neurocranium dorsally, the opercle posteriorly, and the symplectic anteroventrally.” The experts, however, pointed out that not all teleosts have a symplectic, and thus a better formal definition is: “Endochondral bone that is bilaterally paired and articulates with the neurocranium dorsally and the opercle posteriorly.” Generalizations that don’t apply to all teleosts but which might be helpful to ontology users were written for the comments field in the ontology. For hyomandibula we added the comment: “In most teleosts, there is a symplectic, and the hyomandibula articulates with it anteroventrally.” Changes were made to these terms in the TAO by Wasila in the weeks following the meeting and these can be viewed using, e.g., the Bioportal browser (bioportal.org). This was a highly successful way to work through groups of terms, and we plan to do more group ontology development for other skeletal areas at the Joint Meeting of Ichthyologists and Herpetologists in Portland in July 2009.
In the afternoon, we focused the group on data curation, and Jim Balhoff and Peter Midford worked one-on-one with individuals in relation to the web interface and Teleost Taxonomy Ontology, respectively.
Jim Balhoff gave us an overview of the web user interface, and over the course of the afternoon and throughout the meeting, various participants from all of the projects gave him one-on-one feedback on the developing web user interface. Participants who provided feedback on the web interface mockups included Bill Eschmeyer, Sarah Rages, Rick Mayden, Ed Wiley, Eric Hilton, Gloria Arratia, Mark Sabaj-Perez, and Greg Riccardi, from Morphbank. The participants were led through screenshots of a preliminary web interface and suggested changes that would make the interface more usable for them.
During the afternoon, Peter Midford worked with curators on taxonomic issues. Suggested changes (additional synonyms, valid taxa) were made ‘live’ to the Teleost Taxonomy Ontology. Bill Eschmeyer and Stan Blum discussed future updates from CoF and Stan’s interest in the synonym extractor in TTO update with him. Peter also discussed CoF and taxonomy issues with Nicolas Bailly from FishBase. FishBase also imports taxonomy information from CoF.
Concurrently we focused on data curation. Curators were paired with participants who were unfamiliar with the Phenex, our curatorial tool, and they annotated data from papers that were either written by them or in their specific domain of expertise. We also “pre-curated” several papers of interest to the EToL group in order to introduce them to the project.
Paula gave an after dinner talk to the DECAP group, where she introduced Phenoscape and talked about the utility of the database in connecting morphological systematic studies to other data types.
The second day (Saturday) began with a morning of status reports from the various groups constituting DECAP. As Paula had already spoken about Phenoscape the previous evening, Jim and Peter filled Phenoscape’s morning slot with overviews of the informatics component and the TTO respectively. These overviews introduced these topics to DECAP participants who were not involved in Friday’s curation.
Saturday afternoon consisted of breakout groups, one of which was focused on taxonomy and name databasing. The discussion suggests that the TTO may have a role in the larger ichthyological community, as TAO already does. There was also a group focused on future work and a big taxonomy discussion to finish the afternoon.
The remaining two days of the meeting were spent in discussions with ichthyologists on Tree of Life topics, taxonomy and name databases, and issues concerning representing our knowledge about phylogenetic relationships of fishes. All of these topics relate to the synthesis that Phenoscape is trying to achieve, and the conference was of great value to us all.

• Barry Smith – An introduction to ontologies for evolutionary biologists
• Monte Westerfield – Linking animal models and human diseases
• Paula Mabee – Phenoscape: extending model organism ontologies for devo-studies of evolutionary phenotypes
• Wasila Dahdul – Challenges of developing multi-species anatomy ontologies
• Todd Vision – Software and database resources for curation and management of evolutionary phenotypes
• Andy Deans – Developing a Hymenopteran ontology
• Peter Midford – Comparative Analysis of behavior using ontologies
• Anne Maglia – Developing an amphibian ontology

Because the use of ontologies is just emerging in evolutionary biology, we need to work as a community to determine and implement best practices.  The requirements and challenges of creating and using ontologies in evolutionary biology are mainly not unique to the domain, and we can learn a great deal from the logicians, ontologists, and biologists who have connected data using ontologies in the biomedical domain.  This workshop demonstrated how critical and profitable this intersection in knowledge domains promises to be.

A few weeks ago, from Sep 27 to Oct 1, we met in the Black Hills of South Dakota with a group of guest data curators and outside advisors to curate high priority papers, refine the curation workflow and Phenex interface, and evaluate the first prototypes for the web-based user interface to the database. Not only did the workshop end up highly productive (see below), we also had a chance to observe the annual roundup of the largest herd of buffalo in North America, swim in cold Sylvan lake, and see Mount Rushmore one evening.

After participant introductions, the day began with several presentations focused on the utility of synthetic research databases (Monte Westerfield) and the way that phenotype-genotype relationships are handled in model organism databases (Suzanna Lewis, Judy Blake) (for the curious, all presentations are available from the Jamboree agenda page). After a brief description of the Phenoscape data policy (Todd Vision), Jim Balhoff introduced the curation software tool, Phenex, which Wasila Dahdul followed with a hands-on curation exercise that involved using Phenex and associated ontologies to annotate phenotypes (characters) using EQ syntax.

We then paired up our guest data curators with project personnel and got them started.  In order to really focus them on EQ syntax and ontology development, we gave each of our guest curators pre-curated Phenex files containing taxon lists, character matrices and free text character and state descriptions from several important publications authored by the guest data curators themselves or within their area of specialty.

Inevitably, curators spent a significant portion of the time on ontology development.  Many new anatomical and quality entities, along with their relationships and definitions, needed to be added to either the Teleost Anatomy Ontology (TAO) or the Phenotype Ontology (PATO) before characters could be expressed in EQ syntax. In the process of training curators to submit new entities to the term trackers for these ontologies we recognized the need for small, dedicated ontology development meetings (e.g. focused on one anatomical region such as the lateral line system in fishes, or all geometrical or shape qualities).  The better the ontology, the more efficient curation will be.

The curation workflow itself is significantly different in Phenex from the Phenote tool, which we used in the first Data Jamboree. It were the issues brought up there that guided the development of Phenex, and indeed this time we noticed a significant improvement in curatorial efficiency.  We were very pleased that by the end of the workshop, the curators had curated 156 characters (~312 character states) for approximately 150 taxa, resulting in over 45,000 EQ annotations.

One frequent topic of discussion was the depth of annotation granularity to which characters should be curated. For example, many systematic characters pertain to shape, frequently with complex descriptors. These can be curated to a high level (e.g. fin: shape) or to a more granular level (e.g. fin: anterior margin rounded). Judy Blake, one of our outside advisors, pointed out that there is a continuum between use of a structured vocabulary and free text.  A reasonable guideline is to say that data specific to an individual study may not warrant the extra effort with granular annotation and should be left as free-text while data that can be compared across studies should be annotated with ontologies at a rather detailed level.

One observation was that the higher the level of granularity, the more often post-composition is required. The mechanics in using multiple post-composition windows in Phenex was somewhat confusing to guest curators. Another important topic involved the difficulty of not having a universal standard across systematic studies – e.g. descriptors pertaining to size and shape cannot easily be extended across systematic studies. This same issue came up at our previous data jamboree, too. John Lundberg suggested that for comparisons of size within a study, an internal grading of character states (a numbered scale from 1 for smallest and higher numbers corresponding to larger sizes) could be implemented, and this is something that we plan to try.

Following two days of curation, we conducted an experiment to assess curation consistency among our group of curators, and to identify areas where consistency can be improved, for example by better curator training, upfront ontology development, or user interface enhancements. We wanted to determine how often, and for what reasons, curators choose divergent EQ conceptualizations for the same character and character states. Five curators encoded EQ annotations for the same 10 character and state descriptions, using Phenex as the software tool. Immediately afterward we reviewed the results with the group. Notably, only two of the 10 characters were annotated identically among all curators. The reasons for why the other annotations differed revealed different interpretations of shape descriptors, inexperience and unfamiliarity with the ontologies and software, and lack of adequate terms in the ontologies (e.g. shape) as major hurdles towards consistency between curators. Identifying these hurdles helps us to prioritize efforts on visualization tools, ontology development and workflow and Phenex development.

In parallel to the curation activities, we discussed the Teleost Taxonomy Ontology (TTO), taxon concepts, and intermediate synonyms.  Peter Midford has added the intermediate synonyms from the Catalog of Fishes (CoF), but many additional synonyms are present in the literature that must be added. We determined that the need to associate synonyms to their references/publications will require an OBO request for one or more database identifiers. At first we considered using the CoF publication database to generate dbxrefs rather than hunting for DOIs or generating our own, but CoF doesn’t contain many of our publications.  Thus we will need to maintain references and unique identifiers for them in our own database.

In another parallel activity, pairs of participants met with Jim Balhoff and Cartik Kothari  for demonstrations of the web user interface. Jim and Cartik are creating the database and web-application for the research community to explore and query the data. The central gateways for entering the database that emerged from those consultations are querying by gene, anatomy, taxon, or publication. The use case-level query to be implemented first is to find evolutionary phenotypes that match a mutant ZFIN phenotype, or, going in the reverse direction, to find ZFIN mutants for a set of phenotypes that differ between taxa. We plan to be able to demonstrate the first version of the interface at the educational outreach workshop at the SICB meeting on Jan. 6, where we also plan to conduct a first series of usability tests. (For those curious, there was much more feedback and suggestions we received, which we compiled all on the project wiki). 

Working our way towards that meeting over the coming months, we will put into place the first components of a production-level database and a fleshed out query interface. Aside from the software development efforts, we are planning ontology development workshops in small groups in the coming year, for example for TAO and for PATO, and we tentatively aim our next outreach workshop for ASIH 2009. In the meantime, we will need to review our data curation priorities in light of our high priority use cases and proof-of-concept experiments for queries across ZFIN and Phenoscape.

We need to especially thank all our speakers for their excellent presentations, They not only gave the audience a varied introduction to ontologies, but also a set of examples of the integrative questions that can be answered using them.   The slideshows for all of these talks are on our wiki but I thought I would provide a brief overview of each one right below as a summary of the workshop. The use of ontologies is just emerging in evolutionary biology, and it is an exciting time to be involved in this field.  As we move forward to use ontologies in evolutionary biology, we discover new requirements and challenges — for example, the challenge of how we create ontologies that are interoperable — so that we can ask big questions that span not only taxonomic groups (such as bees and fishes and mouse and fly) but different knowledge domains (such as phenotype, evolution, and genetics, genomics, medicine).

So here is an overview of each talk.

Barry Smith (NCBO and Univ. Buffalo) kicked off the workshop with “An Introduction to Ontology for Evolutionary Biology“.  He talked about the GO in relation to “doing biology across the genome”, and he described the domain coverage of the ontologies in the OBO foundry.  He introduced basic ontological concepts and relations, including several new ones that must be made in creating ontology resources for evolutionary biology.  He is currently working with a number of groups including EoL to develop an Environment Ontology (EnvO).

Chris Mungall (Lawrence Berkeley Labs) presented “PATO: The Phenotype and Trait Ontology“.  He focused on why we need ontologies (for example, to solve the data integration problem), introduced “phenotype” and the newly proposed Homologous_to relation. 

Monte Westerfield (Univ. Oregon, Zebrafish Information Network) talked about the use of ontologies in “Linking Animal Models and Human Diseases“.  Just as BLAST can be used to connect animal genes to human genes, shared ontologies and syntax can connect mutant phenotypes to candidate human disease genes. He talked about the importance of curation consistency and how it can be measured and increased.  His proof of principle example, comparing ontology-annotated phenotypes in human and zebrafish demonstrated that genes associated with human diseases can be identified.

It was then my turn to introduce Phenoscape in my talk “An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics“.  Just as animal model phenotypes can be compared to human phenotypes using ontologies, so can animal model phenotypes be compared to phenotypes of multiple species – thus linking comparative evolutionary data to model organism genetics.  I presented several use cases for fishes and described the rapid progress that we have made in developing new ontologies, extending existing ones as well as some of the challenges involved in multispecies ontologies.

Jim Balhoff (NESCent, Phenoscape) presented the software that he has developed for curation of evolutionary phenotypes “Phenote: Curation Software for Evolutionary Phenotypes“.  Originally developed for ontology-based annotation of genetic mutant phenotypes and widely used by model organism curators, Jim described how he has extended and reconfigured Phenote to handle comparative evolutionary data, and he also spoke about his plans to integrate ontology-based phenotype descriptions into the NeXML file format.

Melissa Haendel (Zebrafish Information Network) presented “The Common Anatomy Reference Ontology (CARO) and queries across species“.  She described current anatomy ontologies and why we build them, and the standardization and integration of anatomy ontologies using CARO.  She explained how the issues created by homology can be addressed, including the draft definition of the Homologous_to relationship, and she described how homology data can be used with ontologies to query across species. 

After lunch we had about a ½ hour of “Lightning Talks” during which workshop attendees had an opportunity to introduce themselves and give brief (2-3 minutes) descriptions of their interest in ontologies.  Several attendees seized the chance and made the audience aware of their ontology building efforts.

After that, Ann Maglia (Missouri Univ. of Science and Technology, AmphibAnat) resumed the regular talks and spoke about her group’s work in the “Development of the Amphibian Anatomical Ontology“.  This ontology was driven by the need of the amphibian community to standardize their terminology and thus integrate their comparative work.  She is exploring automated techniques to reduce manual efforts and enhance existing, manually created ontologies.  Ann also described the relational database (RDBOM), the modularization, and web-based community curation methods built by her group and community. 

Martin Ramirez (Museo Argentino de Ciencias Naturales) in his talk “Ontologies, Image Databases, and Evolutionary Biology” described the use of the spider ontology to link images from the spider Tree of Life project to a phylogenetic dataset and a body of image annotation.  He discussed a series of challenges, such as issues involving the alignment of ontologies using homology relations and the “combinability” of ontologies.

Todd Vision (Univ. North Carolina, NESCent), presented “Ontologies and the Identification of Candidate Genes for Complex Traits“.  He considered the qualities of “good” candidate genes and how they are typically discovered and ranked, and then described a test case where ontology terms were used in picking candidate genes computationally (using an approach named CAESAR) for Type 2 Diabetes.  This approach has a promising application for evolutionary traits in non-model organisms.

Peter Midford (Univ. Kansas, Phenoscape) introduced taxonomy ontologies with his talk “Names, Ranks, Clades, and Taxonomy Ontologies” — what’s in them, how they are built and why one would use one.  The issue of what species are ontologically, more specifically whether species are classes or instances or both, impacts not only the way an ontology is built but also what kinds of assertions can be inferred or not.

Suzanna Lewis (Lawrence Berkeley Lab, BBOP) and I wrapped up by listing some of the challenges for the evolutionary biology community that became apparent over the day. 

Especially prominent was the need for communication among evolutionary biologists developing ontologies so that they can be developed from the outset to be interoperable.  This and many related comments from attendees suggested that an NSF-RCN (Research Coordination Network) proposal might be the best next step and an effective mechanism to fund and promote communication among and between evolutionary biologists, ontologists, and model organism biologists.

As a result, we are now beginning to gather ideas, objectives, and possible participants for an RCN proposal. If you have thoughts on this, or if you are interested in participating, we would love to hear from you – leave a comment here, or email me (pmabee{at}usd{dot}edu).

We have three overall goals with the Data Jamboree. The first is to train fish morphologists outside of our project to understand how to use the tools (primarily Phenote) and ontologies to generate phenotype annotations compliant with the EQ approach. 

The second is to develop, review and where necessary refine best practices guidelines for annotation, to ensure that different morphologist generate the same, or at least semantically equivalent phenotype assertions from the same character descriptions.

The third goal is to generate actual data. Hence, after an initial training exercise, over the next two and a half days the morphologists and our curators will be going over a pre-selected set of publications and translate the character descriptions into EQ-compliant assertions, and the informaticists among us as well as our advisors will look over their shoulders to see what needs refinement.